Mercurial > repos > recetox > matchms_split
comparison matchms_split.py @ 14:114617e6ad33 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit da193865f41a3a840ecc4ba0afab1d358554998a
author | recetox |
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date | Mon, 05 Feb 2024 10:35:49 +0000 |
parents | 0cf68b536cd1 |
children |
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13:fc1bc38ede0b | 14:114617e6ad33 |
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1 import argparse | 1 import argparse |
2 import itertools | 2 import itertools |
3 import os | 3 import os |
4 from typing import List | |
5 | 4 |
5 import matchms | |
6 from matchms.exporting import save_as_msp | 6 from matchms.exporting import save_as_msp |
7 from matchms.importing import load_from_msp | 7 from matchms.importing import load_from_msp |
8 | 8 |
9 | 9 |
10 def get_spectra_names(spectra: list) -> List[str]: | 10 matchms.Metadata.set_key_replacements({}) |
11 """Read the keyword 'compound_name' from a spectra. | |
12 | |
13 Args: | |
14 spectra (list): List of individual spectra. | |
15 | |
16 Returns: | |
17 List[str]: List with 'compoud_name' of individual spectra. | |
18 """ | |
19 return [x.get("compound_name") for x in spectra] | |
20 | 11 |
21 | 12 |
22 def make_outdir(outdir: str): | 13 def make_outdir(outdir: str): |
23 """Create destination directory. | 14 """Create destination directory. |
24 | 15 |
33 | 24 |
34 Args: | 25 Args: |
35 spectra (List[Spectrum]): Spectra to write to file | 26 spectra (List[Spectrum]): Spectra to write to file |
36 outdir (str): Path to destination directory. | 27 outdir (str): Path to destination directory. |
37 """ | 28 """ |
38 names = get_spectra_names(spectra) | |
39 for i in range(len(spectra)): | 29 for i in range(len(spectra)): |
40 outpath = assemble_outpath(names[i], outdir) | 30 save_as_msp(spectra[i], os.path.join(outdir, f"{i}.msp")) |
41 save_as_msp(spectra[i], outpath) | |
42 | |
43 | |
44 def assemble_outpath(name, outdir): | |
45 """Filter special chracteres from name. | |
46 | |
47 Args: | |
48 name (str): Name to be filetered. | |
49 outdir (str): Path to destination directory. | |
50 """ | |
51 filename = ''.join(filter(str.isalnum, name)) | |
52 outfile = str(filename) + ".msp" | |
53 outpath = os.path.join(outdir, outfile) | |
54 return outpath | |
55 | 31 |
56 | 32 |
57 def split_round_robin(iterable, num_chunks): | 33 def split_round_robin(iterable, num_chunks): |
58 chunks = [list() for _ in range(num_chunks)] | 34 chunks = [list() for _ in range(num_chunks)] |
59 index = itertools.cycle(range(num_chunks)) | 35 index = itertools.cycle(range(num_chunks)) |
74 method = args.method | 50 method = args.method |
75 parameter = args.parameter | 51 parameter = args.parameter |
76 | 52 |
77 | 53 |
78 if __name__ == "__main__": | 54 if __name__ == "__main__": |
79 spectra = load_from_msp(filename, metadata_harmonization=True) | 55 spectra = load_from_msp(filename, metadata_harmonization=False) |
80 make_outdir(outdir) | 56 make_outdir(outdir) |
81 | 57 |
82 if method == "one-per-file": | 58 if method == "one-per-file": |
83 write_spectra(list(spectra), outdir) | 59 write_spectra(list(spectra), outdir) |
84 else: | 60 else: |